Transcriptomic response of Arabidopsis thaliana (L.) Heynh. roots to ibuprofen

References

• Abhilash PC, Jamil S, Singh N. 2009. Transgenic plants for enhanced biodegradation and phytoremediation of organic xenobiotics. Biotechnol Adv 27:474–488.
   PubMed Web of Science ®Google Scholar
• Aguirre-Martinez GV, DelValls AT, Laura Martín-Diaz M. 2015. Yes, caffeine, ibuprofen, carbamazepine, novobiocin and tamoxifen have an effect on Corbicula fluminea (Müller, 1774). Ecotoxicol Environ Saf 120:142–154.
   PubMed Web of Science ®Google Scholar
• Baerson SR, Sanchez-Moreiras A, Pedrol-Bonjoch N, Schulz M, Kagan IA, Agarwal AK, Reigosa MJ, Duke SO. 2005. Detoxification and transcriptome response in Arabidopsis seedlings exposed to the allelochemical benzoxazolin-2(3H)-one. J Biol Chem 280:21867–21881.
   PubMed Web of Science ®Google Scholar
• Bessone F. 2010. Non-steroidal anti-inflammatory drugs: What is the actual risk of liver damage? World J Gastroenterol 16:5651–5661.
   PubMed Web of Science ®Google Scholar
• Buser H-R, Poiger T, Müller MD. 1999. Occurrence and environmental behavior of the chiral pharmaceutical drug ibuprofen in surface waters and in wastewater. Environ Sci Technol 33:2529–2535.
   Web of Science ®Google Scholar
• Chehrenegar B, Hu J, Ong SL. 2016. Active removal of ibuprofen by Money plant enhanced by ferrous ions. Chemosphere 144:91–96.
   PubMed Web of Science ®Google Scholar
• Coleman J, Blake-Kalff M, Davies E. 1997. Detoxification of xenobiotics by plants: chemical modification and vacuolar compartmentation. Trends Plant Sci 2:144–151.
   Web of Science ®Google Scholar
• Ekman DR, Lorenz WW, Przybyla AE, Wolfe NL, Dean JF. 2003. SAGE analysis of transcriptome responses in Arabidopsis roots exposed to 2,4,6-trinitrotoluene. Plant Physiol 133:1397–1406.
   PubMed Web of Science ®Google Scholar
• Eslami A, Amini MM, Yazdanbakhsh AR, Rastkari N, Mohseni-Bandpei A, Nasseri S, Piroti E, Asadi A. 2015. Occurrence of non-steroidal anti-inflammatory drugs in Tehran source water, municipal and hospital wastewaters, and their ecotoxicological risk assessment. Environ Monit Assess 187:734.
   PubMed Web of Science ®Google Scholar
• Fent K, Weston AA, Caminada D. 2006. Ecotoxicology of human pharmaceuticals. Aquat Toxicol 76:122–159.
   PubMed Web of Science ®Google Scholar
• Gandia-Herrero F, Astrid L, Larson T, Graham IA, Bowles DJ, Rylott EL, Bruce NC. 2008. Detoxification of the explosive 2,4,6-trinitrotoluene in Arabidopsis: discovery of bifunctional O- and C-glucosyltransferases. Plant J 56:963–974.
   PubMed Web of Science ®Google Scholar
• Garcia T, Gutierrez J, Veloso J, Gago-Fuentes R, Diaz J. 2015. Wounding induces local resistance but systemic susceptibility to Botrytis cinerea in pepper plants. J Plant Physiol 176:202–209.
   PubMed Web of Science ®Google Scholar
• Gao S, Guo W, Feng W, Liu L, Song X, Chen J, Hou W, Zhu H, Tang S, Hu J. 2016. LTP3 contributes to disease susceptibility in Arabidopsis by enhancing abscisic acid (ABA) biosynthesis. Mol Plant Pathol 17:412–426.
   PubMed Web of Science ®Google Scholar
• Gomez MJ, Martinez Bueno MJ, Lacorte S, Fernández-Alba AR, Aguera A. 2007. Pilot survey monitoring pharmaceuticals and related compounds in a sewage treatment plant located on the Mediterranean coast. Chemosphere 66:993–1002.
   PubMed Web of Science ®Google Scholar
• Gunning V, Tzafestas K, Sparrow H, Johnston EJ, Brentnall AS, Potts JR, Rylott EL, Bruce NC. 2014. Arabidopsis glutathione transferases U24 and U25 exhibit a range of detoxification activities with the environmental pollutant and explosive, 2,4,6-trinitrotoluene. Plant Physiol 165:854–865.
   PubMed Web of Science ®Google Scholar
• Hamman MA, Thompson GA, Hall SD. 1997. Regioselective and stereoselective metabolism of ibuprofen by human cytochrome P450 2C. Biochem Pharmacol 54:33–41.
   PubMed Web of Science ®Google Scholar
• Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. 2007. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8:R19.
   PubMed Web of Science ®Google Scholar
• Hoagland DR. 1920. Optimum nutrient solutions for plants. Science 52:562–564.
   PubMedGoogle Scholar
• Hijosa-Valsero M, Matamoros V, Sidrach-Cardona R, Martín-Villacorta J, Bécares E, Bayona JM. 2010. Comprehensive assessment of the design configuration of constructed wetlands for the removal of pharmaceuticals and personal care products from urban wastewaters. Water Res 44:3669–3678.
   PubMed Web of Science ®Google Scholar
• Ibanez S, Talano M, Ontanon O, Suman J, Medina MI, Macek T, Agostini El. 2016. Transgenic plants and hairy roots: exploiting the potential of plant species to remediate contaminants. New Biotechnol 33:625–635.
   PubMed Web of Science ®Google Scholar
• Iori V, Zacchini M, Pietrini F. 2013. Growth, physiological response and phytoremoval capability of two willow clones exposed to ibuprofen under hydroponic culture. J Hazard Mater 262:796–804.
   PubMed Web of Science ®Google Scholar
• Jeffries KM, Brander SM, Britton MT, Fangue NA, Connon RE. 2015. Chronic exposures to low and high concentrations of ibuprofen elicit different gene response patterns in a euryhaline fish. Environ Sci Pollut Res 22:17397–17413.
   PubMed Web of Science ®Google Scholar
• Kotowska U, Kapelewska J, Sturgulewska J. 2014. Determination of phenols and pharmaceuticals in municipal wastewaters from Polish treatment plants by ultrasound-assisted emulsification–microextraction followed by GC–MS. Environ Sci Pollut Res 21:660–673.
   PubMed Web of Science ®Google Scholar
• Kotyza J, Soudek P, Kafka Z, Vanek T. 2010. Phytoremediation of pharmaceuticals—preliminary study. Int J Phytoremediation 12:306–316.
   PubMed Web of Science ®Google Scholar
• Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210.
   PubMed Web of Science ®Google Scholar
• Lamoureux GL, Rusness DG. 1993. Glutathione in the metabolism and detoxification of xenobiotics in plants. In: De Kok LJ, Stulen I, Rennenberg H, Brunold C, Reuser W, editors. Sulfur nutrition and assimilation in higher plants. The Hague: SPB Academic Publishing. p. 221–237.
   Google Scholar
• Lim EK, Ashford DA, Hou B, Jackson RG, Bowles DJ. 2004. Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides. Biotechnol Bioeng 87:623–631.
   PubMed Web of Science ®Google Scholar
• Ma W, Smigel A, Tsai YC, Braam J, Berkowitz GA. 2008. Innate immunity signaling: cytosolic Ca2+ elevation is linked to downstream nitric oxide generation through the action of calmodulin or a calmodulin-like protein. Plant Physiol 148:818–828.
   PubMed Web of Science ®Google Scholar
• Marsik P, Soudek P, Hudcova T, Syrovatka J, Vanek T. 2015. Pharmaceuticals in domestic and agricultural waste waters - Problem and its solution. Water Pract Technol 10:564–572.
   Google Scholar
• Masksymiec W, Krupa Z. 2007. Effects of methyl jasmonate and excess copper on root and leaf growth. Biol Plantarum 51:322–326.
   Web of Science ®Google Scholar
• Nojiri H, Sugimori M, Yamane H, Nishimura Y, Yamada A, Shibuya N, Kodama O, Murofushi N, Omori T. 1996. Involvement of jasmonic acid in elicitor-induced phytoalexin production in suspension-cultured rice cells. Plant Physiol 110:387–392.
   PubMed Web of Science ®Google Scholar
• Pietrini F, Di Baccio D, Acena J, Perez S, Barcelo D, Zacchini M. 2015. Ibuprofen exposure in Lemna gibba L.: evaluation of growth and phytotoxic indicators, detection of ibuprofen and identification of its metabolites in plant and in the medium. J Hazard Mater 300:189–193.
   PubMed Web of Science ®Google Scholar
• Provart NJ, Zhu T. 2003. A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol 2003:271–272.
   Google Scholar
• Rajeevan MS, Vernon SD, Taysavang N, Unger ER. 2001. Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J Mol Diagn 3:26–31.
   PubMed Web of Science ®Google Scholar
• Rapala-Kozik M, Wolak N, Kujda M, Banas AK. 2012. The upregulation of thiamine (vitamin B1) biosynthesis in A. thaliana seedlings under salt and osmotic stress conditions is mediated by abscisic acid at the early stages of this stress response. BMC Plant Biol 12:2.
   PubMed Web of Science ®Google Scholar
• Roberts PH, Thomas KV. 2006. The occurrence of selected pharmaceuticals in wastewater effluent and surface waters of the lower Tyne catchment. Sci Total Environ 356:143–153.
   PubMed Web of Science ®Google Scholar
• Sadezky A, Loffler D, Schlusener M, Roig B, Ternes T. 2010. Real Sitution: occurrence of the main investigated PPs in water bodies. In. Roig B, editor. Pharmaceuticals in the Environment: current knowledge and need assessment to reduce presence and impact. London: IWA Publishing. p. 198.
   Google Scholar
• Sanchez-Fernandez R, Davies TG, Coleman JO, Rea PA. 2001. The Arabidopsis thaliana ABC protein superfamily: a complete inventory. J Biol Chem 276:30231–30244.
   PubMed Web of Science ®Google Scholar
• Schroder P, Collins C. 2002. Conjugating enzymes involved in xenobiotic metabolism of organic xenobiotics in plants. Int J Phytoremediation 4:247–265.
   Web of Science ®Google Scholar
• Schulz B, Kolukisaoglu HU. 2006. Genomics of plant ABC transporters: the alphabet of photosynthetic life forms or just holes in membranes? FEBS Lett 580:1010–1016.
   PubMed Web of Science ®Google Scholar
• Shan C, Liang Z. 2010. Jasmonic acid regulates ascorbate and glutathione metabolism in Agropyron cristatum leaves under water stress. Plant Sci 178:130–139.
   Web of Science ®Google Scholar
• Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:1–25.
   PubMedGoogle Scholar
• Smyth GK, Michaud J, Scott H. 2005. The use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21:2067–2075.
   PubMed Web of Science ®Google Scholar
• Smyth GK, Speed TP. 2003. Normalization of cDNA microarray data. Methods 31:265–273.
   PubMed Web of Science ®Google Scholar
• Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E. 2008. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014.
   PubMed Web of Science ®Google Scholar
• Truisi GL, Consiglio ED, Parmentier C, Savary CC, Pomponio G, Bois F, Lauer B, Jossé R, Hewitt PG, Mueller SO, Richert L, Guillouzo A, Testai E. 2015. Understanding the biokinetics of ibuprofen after single and repeated treatments in rat and human in vitro liver cell systems. Toxicol Lett 233:172–186.
   PubMed Web of Science ®Google Scholar
• Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35:W71–W74.
   PubMed Web of Science ®Google Scholar
• Van Aken B. 2009. Transgenic plants for enhanced phytoremediation of toxic explosives. Curr Opin Biotechnol 20:231–236.
   PubMed Web of Science ®Google Scholar
• Van Aken B, Correa PA, Schnoor JL. 2010. Phytoremediation of polychlorinated biphenyls: new trends and promises. Environ Sci Technol 44:2767–2776.
   PubMed Web of Science ®Google Scholar
• Widdup EE, Chatfield-Reed K, Henry D, Chua G, Samuel MA, Muench DG. 2015. Identification of detoxification pathways in plants that are regulated in response to treatment with organic compounds isolated from oil sands process-affected water. Chemosphere 139:47–53.
   PubMed Web of Science ®Google Scholar
• Willits MG, Giovanni M, Prata RTN, Kramer CM, De Luca V, Steffens JC, Graser G. 2004. Bio-fermentation of modified flavonoids: an example of in vivo diversification of secondary metabolites. Phytochemistry 65:31–41.
   PubMed Web of Science ®Google Scholar
• Xie YD, Li W, Guo D, Dong J, Zhang Q, Fu Y, Ren D, Peng M, Xia Y. 2010. The Arabidopsis gene SIGMA FACTOR-BINDING PROTEIN 1 plays a role in the salicylate- and jasmonate-mediated defence responses. Plant Cell Environ 33:828–839.
   PubMed Web of Science ®Google Scholar
• Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K. 2008. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20:2160–2176.
   PubMed Web of Science ®Google Scholar
• Zuker M, Mathews DH, Turner DH. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J, Clark BFC, editors. RNA biochemistry and biotechnology. Dordrecht, NL: Kluwer Academic Publishers. p. 11–43.
   Google Scholar